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Example Data Sets

SequenceData

A number of data files are stored locally in: /research/sequences/GenBank/blast/db/

There are these standard NCBI blast files:

 16SMicrobial
 est_human
 est_mouse
 human_genomic
 human_genomic_transcript
 mouse_genomic_transcript
 nr
 nt
 other_genomic
 refseqgene
 refseq_genomic
 refseq_protein
 refseq_rna
 sts
 swissprot
 vector

For zebrafish in /research/sequences/GenBank/D_rerio/db/

 dr_ref_Zv9_chr1
 dr_ref_Zv9_chr10
 dr_ref_Zv9_chr11
 dr_ref_Zv9_chr12
 dr_ref_Zv9_chr13
 dr_ref_Zv9_chr14
 dr_ref_Zv9_chr15
 dr_ref_Zv9_chr16
 dr_ref_Zv9_chr17
 dr_ref_Zv9_chr18
 dr_ref_Zv9_chr19
 dr_ref_Zv9_chr2
 dr_ref_Zv9_chr20
 dr_ref_Zv9_chr21
 dr_ref_Zv9_chr22
 dr_ref_Zv9_chr23
 dr_ref_Zv9_chr24
 dr_ref_Zv9_chr25
 dr_ref_Zv9_chr3
 dr_ref_Zv9_chr4
 dr_ref_Zv9_chr5
 dr_ref_Zv9_chr6
 dr_ref_Zv9_chr7
 dr_ref_Zv9_chr8
 dr_ref_Zv9_chr9
 dr_ref_Zv9_chrMT
 dr_ref_Zv9_unplaced
 protein
 pseudo_without_product
 rna

To help identify things that may not belong in your data: /research/sequences/misc/

 contaminant.fasta  
 contaminant.txt
 UniVec  
 UniVec_Core

Also Bowtie indexes: /research/bowtie_indexes/

 c_elegans_ws200
 contaminant
 d_melanogaster_fb5_22
 d_rerio_ZV9_62
 e_coli
 h_sapiens_37_asm
 m_musculus_ncbi37
 rn4
 s_cerevisiae
 vector